--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/bs_seeker2-align.py	Fri Jul 12 18:47:28 2013 -0400
@@ -0,0 +1,349 @@
+#!/usr/bin/python
+
+from optparse import OptionParser, OptionGroup
+import re
+import tempfile
+from bs_align import output
+from bs_align.bs_pair_end import *
+from bs_align.bs_single_end import *
+from bs_align.bs_rrbs import *
+from bs_utils.utils import *
+
+
+if __name__ == '__main__':
+
+    parser = OptionParser()
+    # option group 1
+    opt_group = OptionGroup(parser, "For single end reads")
+    opt_group.add_option("-i", "--input", type="string", dest="infilename",help="Input your read file name (FORMAT: sequences, fastq, qseq,fasta)", metavar="INFILE")
+    parser.add_option_group(opt_group)
+
+    # option group 2
+    opt_group = OptionGroup(parser, "For pair end reads")
+    opt_group.add_option("-1", "--input_1", type="string", dest="infilename_1",help="Input your read file end 1 (FORMAT: sequences, qseq, fasta, fastq)", metavar="FILE")
+    opt_group.add_option("-2", "--input_2", type="string", dest="infilename_2",help="Input your read file end 2 (FORMAT: sequences, qseq, fasta, fastq)", metavar="FILE")
+    opt_group.add_option("--minins",type = "int",dest = "min_insert_size", help="The minimum insert size for valid paired-end alignments [Default: %default]", default = -1)
+    opt_group.add_option("--maxins",type = "int",dest = "max_insert_size", help="The maximum insert size for valid paired-end alignments [Default: %default]", default = 400)
+    parser.add_option_group(opt_group)
+
+    # option group 3
+    opt_group = OptionGroup(parser, "Reduced Representation Bisulfite Sequencing Options")
+    opt_group.add_option("-r", "--rrbs", action="store_true", dest="rrbs", default = False, help = 'Process reads from Reduced Representation Bisulfite Sequencing experiments')
+    opt_group.add_option("-c", "--cut-site", type="string",dest="cut_format", help="Cutting sites of restriction enzyme. Ex: MspI(C-CGG), Mael:(C-TAG), double-enzyme MspI&Mael:(C-CGG,C-TAG). [Default: %default]", metavar="pattern", default = "C-CGG")
+    opt_group.add_option("-L", "--low", type = "int", dest="rrbs_low_bound", help="lower bound of fragment length (excluding C-CGG ends) [Default: %default]", default = 40)
+    opt_group.add_option("-U", "--up", type = "int", dest="rrbs_up_bound", help="upper bound of fragment length (excluding C-CGG ends) [Default: %default]", default = 500)
+    parser.add_option_group(opt_group)
+
+    # option group 4
+    opt_group = OptionGroup(parser, "General options")
+    opt_group.add_option("-t", "--tag", type="string", dest="taginfo",help="[Y]es for undirectional lib, [N]o for directional [Default: %default]", metavar="TAG", default = 'N')
+    opt_group.add_option("-s","--start_base",type = "int",dest = "cutnumber1", help="The first base of your read to be mapped [Default: %default]", default = 1)
+    opt_group.add_option("-e","--end_base",type = "int",dest = "cutnumber2", help="The last cycle number of your read to be mapped [Default: %default]", default = 200)
+    opt_group.add_option("-a", "--adapter", type="string", dest="adapter_file",help="Input text file of your adaptor sequences (to be trimed from the 3'end of the reads). Input 1 seq for dir. lib., 2 seqs for undir. lib. One line per sequence", metavar="FILE", default = '')
+    opt_group.add_option("--am",type = "int",dest = "adapter_mismatch", help="Number of mismatches allowed in adaptor [Default: %default]", default = 0)
+    opt_group.add_option("-g", "--genome", type="string", dest="genome",help="Name of the reference genome (the same as the reference genome file in the preprocessing step) [ex. chr21_hg18.fa]")
+    opt_group.add_option("-m", "--mismatches",type = "int", dest="int_no_mismatches",help="Number of mismatches in one read [Default: %default]", default = 4)
+    opt_group.add_option("--aligner", dest="aligner",help="Aligner program to perform the analisys: " + ', '.join(supported_aligners) + " [Default: %default]", metavar="ALIGNER", default = BOWTIE2)
+    opt_group.add_option("-p", "--path", dest="aligner_path", help="Path to the aligner program. Defaults: " +' '*70+ '\t'.join(('%s: %s '+' '*70) % (al, aligner_path[al]) for al in sorted(supported_aligners)),
+        metavar="PATH"
+    )
+    opt_group.add_option("-d", "--db", type="string", dest="dbpath",help="Path to the reference genome library (generated in preprocessing genome) [Default: %default]" , metavar="DBPATH", default = reference_genome_path)
+    opt_group.add_option("-l", "--split_line",type = "int", dest="no_split",help="Number of lines per split (the read file will be split into small files for mapping. The result will be merged. [Default: %default]", default = 4000000)
+    opt_group.add_option("-o", "--output", type="string", dest="outfilename",help="The name of output file [INFILE.bs(se|pe|rrbs)]", metavar="OUTFILE")
+    opt_group.add_option("-f", "--output-format", type="string", dest="output_format",help="Output format: "+', '.join(output.formats)+" [Default: %default]", metavar="FORMAT", default = output.BAM)
+    opt_group.add_option("--no-header", action="store_true", dest="no_SAM_header",help="Suppress SAM header lines [Default: %default]", default = False)
+    opt_group.add_option("--temp_dir", type="string", dest="temp_dir",help="The path to your temporary directory [Default: %default]", metavar="PATH", default = tempfile.gettempdir())
+    opt_group.add_option("--XS",type = "string", dest="XS_filter",help="Filter definition for tag XS, format X,Y. X=0.8 and y=5 indicate that for one read, if #(mCH sites)/#(all CH sites)>0.8 and #(mCH sites)>5, then tag XS=1; or else tag XS=0. [Default: %default]", default = "0.5,5") # added by weilong
+    opt_group.add_option("--multiple-hit", action="store_true", dest="Output_multiple_hit", default = False, help = 'Output reads with multiple hits to file\"Multiple_hit.fa\"')
+
+    opt_group.add_option("-v", "--version", action="store_true", dest="version",help="show version of BS-Seeker2", metavar="version", default = False)
+
+    parser.add_option_group(opt_group)
+
+    # option group 5
+    opt_group = OptionGroup(parser, "Aligner Options",
+        "You may specify any additional options for the aligner. You just have to prefix them with " +
+        ', '.join('%s for %s' % (aligner_options_prefixes[aligner], aligner) for aligner in supported_aligners)+
+        ', and BS Seeker will pass them on. For example: --bt-p 4 will increase the number of threads for bowtie to 4, '
+        '--bt--tryhard will instruct bowtie to try as hard as possible to find valid alignments when they exist, and so on. '
+        'Be sure that you know what you are doing when using these options! Also, we don\'t do any validation on the values.')
+    parser.add_option_group(opt_group)
+
+
+    #----------------------------------------------------------------
+    # separate aligner options from BS Seeker options
+    aligner_options = {}
+    bs_seeker_options = []
+    i = 1
+    while i < len(sys.argv):
+        arg = sys.argv[i]
+        m = re.match(r'^%s' % '|'.join('(%s)'% aligner_options_prefixes[al] for al in supported_aligners), arg)
+        if m:
+            a_opt = arg.replace(m.group(0),'-',1)
+            aligner_options[a_opt] = []
+            while i + 1 < len(sys.argv) and sys.argv[i+1][0] != '-':
+                aligner_options[a_opt].append(sys.argv[i+1])
+                i += 1
+            if len(aligner_options[a_opt]) == 0: # if it is a key-only option
+                aligner_options[a_opt] = True
+        else:
+            bs_seeker_options.append(arg)
+        i += 1
+
+
+    (options, args) = parser.parse_args(args = bs_seeker_options)
+
+
+    # if no options were given by the user, print help and exit
+    if len(sys.argv) == 1:
+        print parser.print_help()
+        exit(0)
+
+    if options.version :
+        show_version()
+        exit (-1)
+    else :
+        show_version()
+
+    # check parameters
+    # input read files
+    if options.infilename and (options.infilename_1 or options.infilename_2):
+        error('-i and [-1|-2] options are exclusive. You should use only one of them.')
+
+    if not (options.infilename or (options.infilename_1 and options.infilename_2)):
+        error('You should set either -i or -1 and -2 options.')
+    # -t, directional / un-directional library
+    asktag=str(options.taginfo).upper()
+    if asktag not in 'YN':
+        error('-t option should be either Y or N, not %s' % asktag)
+    # -a
+    if options.aligner not in supported_aligners:
+        error('-a option should be: %s' % ' ,'.join(supported_aligners)+'.')
+    # path for aligner
+    aligner_exec = os.path.expanduser( os.path.join(options.aligner_path or aligner_path[options.aligner], options.aligner) )
+    # mismatch allowed: bowtie 1,build-in parameter '-m'; bowtie 2, post-filter paramter
+    # mismatch should no greater than the read length
+    int_no_mismatches=min(options.int_no_mismatches, options.cutnumber2-options.cutnumber1)
+    str_no_mismatches=str(int_no_mismatches)
+    # -g
+    if options.genome is None:
+        error('-g is a required option')
+    genome = os.path.split(options.genome)[1]
+    genome_subdir = genome
+
+    # try to guess the location of the reference genome for RRBS
+    if options.rrbs:
+        if options.rrbs_low_bound and options.rrbs_up_bound:
+            if options.cut_format == "C-CGG" :
+                genome_subdir += '_rrbs_%d_%d'  % (options.rrbs_low_bound, options.rrbs_up_bound)
+            else :
+                genome_subdir += '_rrbs_%s_%d_%d'  % ( re.sub(",","-",re.sub("-", "", options.cut_format)), options.rrbs_low_bound, options.rrbs_up_bound)
+        else:
+            possible_refs = filter(lambda dir: dir.startswith(genome+'_rrbs_'), os.listdir(options.dbpath))
+            if len(possible_refs) == 1:
+                genome_subdir = possible_refs[0]
+            else:
+                error('Cannot localize unambiguously the reference genome for RRBS. '
+                      'Please, specify the options \"--low\" and \"--up\" that you used at the index-building step.\n'
+                      'Possible choices are:\n' + '\n'.join([pr.split('_rrbs_')[-1].replace('_',', ') for pr in possible_refs]))
+
+    db_path = os.path.expanduser(os.path.join(options.dbpath, genome_subdir + '_' + options.aligner))
+
+    if not os.path.isdir(db_path):
+        error('Index DIR \"' + genome_subdir + '..\" cannot be found in ' + options.dbpath +'.\n\tPlease run the bs_seeker2-build.py '
+                            'to create it with the correct parameters for -g, -r, --low, --up and --aligner.')
+
+    # handle aligner options
+    #
+
+    # default aligner options
+    aligner_options_defaults = {
+                                BOWTIE  : { '-e'              : 40*int_no_mismatches,
+                                            '--nomaqround'    : True,
+                                            '--norc'          : True,
+                                            '-k'              : 2,
+                                            # -k=2; report two best hits, and filter by error rates
+                                            '--quiet'         : True,
+                                            '--best'          : True,
+#                                            '--suppress'      : '2,5,6',
+                                            '--sam'           : True,
+                                            '--sam-nohead'    : True,
+                                            '-p'              : 2
+                                },
+                                BOWTIE2 : {
+                                            #'-M'              : 5,
+                                            '--norc'          : True,
+                                            '--quiet'         : True,
+                                            '-p'              : 2,
+                                            '--sam-nohead'    : True,
+                                            # run bowtie2 in local mode by default
+                                            '--local' : '--end-to-end' not in aligner_options,
+                                            #'--mm'            : True,
+                                            '-k'              : 2
+                                },
+                                SOAP    : { '-v' : int_no_mismatches,
+                                            '-p' : 2,
+                                            '-r' : 2,
+                                            '-M' : 4
+                                          },
+                                RMAP    : { '-M' : 2
+                                            # to do # control for only mapping on + strand
+                                          }
+
+                                }
+
+    if '--end-to-end' not in aligner_options:
+        aligner_options_defaults[BOWTIE2].update({'-D' : 50})
+        #aligner_options_defaults[BOWTIE2].update({'-D' : 50, '-R': 3, '-N': 0, '-L': 15, '-i' : 'S,1,0.50'})
+    else:
+        aligner_options_defaults[BOWTIE2].update({'-D' : 50, '-L': 15, '--score-min': 'L,-0.6,-0.6' })
+
+    aligner_options = dict(aligner_options_defaults[options.aligner], **aligner_options)
+
+    aligner_options_string = lambda : ' %s ' % (' '.join(opt_key +
+                                                         (' ' + ' '.join(map(str,opt_val)) # join all values if the value is an array
+                                                          if type(opt_val) is list else
+                                                                ('' if type(opt_val) is bool and opt_val # output an empty string if it is a key-only option
+                                                                 else ' ' +str(opt_val)) # output the value if it is a single value
+                                                         )
+                                                        for opt_key, opt_val in aligner_options.iteritems() if opt_val not in [None, False]))
+
+
+#    tmp_path = (options.outfilename or options.infilename or options.infilename_1) +'-'+ options.aligner+ '-TMP'
+#    clear_dir(tmp_path)
+
+    if options.output_format not in output.formats:
+        error('Output format should be one of: ' + ', '.join(output.formats))
+
+    if options.outfilename:
+        outfilename = options.outfilename
+        logfilename = outfilename
+    elif options.infilename is not None:
+        logfilename = options.infilename+'_'+ ('rr' if options.rrbs else '') + 'bsse'
+        outfilename = logfilename + '.' + options.output_format
+    else:
+        logfilename = options.infilename_1+'_'+ ('rr' if options.rrbs else '') + 'bspe'
+        outfilename = logfilename + '.' + options.output_format
+
+    outfilename = os.path.expanduser(outfilename)
+    logfilename = os.path.expanduser(logfilename)
+    outfile = output.outfile(outfilename, options.output_format, deserialize(os.path.join(db_path, 'refname')), ' '.join(sys.argv), options.no_SAM_header)
+
+    open_log(logfilename+'.bs_seeker2_log')
+
+    aligner_title = options.aligner
+    if options.aligner == BOWTIE2 :
+        if '--end-to-end' in aligner_options :
+            aligner_title = aligner_title + "-e2e"
+        else:
+            aligner_title = aligner_title + "-local"
+
+    tmp_path = tempfile.mkdtemp(prefix='bs_seeker2_%s_-%s-TMP-' % (os.path.split(outfilename)[1], aligner_title ), dir = options.temp_dir)
+
+
+    (XS_x, XS_y) = options.XS_filter.split(",")
+    XS_pct = float(XS_x)
+    XS_count = int(XS_y)
+    logm('Filter for tag XS: #(mCH)/#(all CH)>%f and #(mCH)>%d' % (XS_pct, XS_count))
+
+
+    logm('Temporary directory: %s' % tmp_path)
+    logm('Reduced Representation Bisulfite Sequencing: %s' % str(options.rrbs))
+    if options.infilename is not None:
+        logm('Single end')
+
+        aligner_command = aligner_exec  + aligner_options_string() + \
+                              { BOWTIE   : ' %(reference_genome)s  -f %(input_file)s %(output_file)s',
+                                BOWTIE2  : ' -x %(reference_genome)s -f -U %(input_file)s -S %(output_file)s',
+                                SOAP     : ' -D %(reference_genome)s.fa.index -o %(output_file)s -a %(input_file)s',
+                                RMAP     : ' -c %(reference_genome)s.fa -o %(output_file)s %(input_file)s'
+                              }[options.aligner]
+        logm ('Aligner command: %s' % aligner_command)
+        # single end reads
+        if options.rrbs: # RRBS scan
+            bs_rrbs(options.infilename,
+                    asktag,
+            #        options.rrbs_taginfo,
+                    options.adapter_file,
+                    options.cutnumber1,
+                    options.cutnumber2,
+                    options.no_split,
+                    str_no_mismatches,
+                    aligner_command,
+                    db_path,
+                    tmp_path,
+                    outfile,
+                    XS_pct,
+                    XS_count,
+                    options.adapter_mismatch,
+                    options.cut_format,
+                    options.Output_multiple_hit
+                    )
+        else: # Normal single end scan
+            bs_single_end(  options.infilename,
+                            asktag,
+                            options.adapter_file,
+                            options.cutnumber1,
+                            options.cutnumber2,
+                            options.no_split,
+                            str_no_mismatches,
+                            aligner_command,
+                            db_path,
+                            tmp_path,
+                            outfile,
+                            XS_pct,
+                            XS_count,
+                            options.adapter_mismatch,
+                            options.Output_multiple_hit
+                            )
+    else:
+        logm('Pair end')
+        # pair end specific default options
+        aligner_options = dict({BOWTIE: {'--ff'  : asktag == 'N',
+                                         '--fr'  : asktag == 'Y',
+                                         '-X'    : options.max_insert_size,
+                                         '-I'    : options.min_insert_size if options.min_insert_size > 0 else None
+                                },
+                                BOWTIE2 : {
+                                         '--ff'  : asktag == 'N',
+                                         '--fr'  : asktag == 'Y',
+                                         '-X'    : options.max_insert_size,
+                                         '-I'    : options.min_insert_size if options.min_insert_size > 0 else None,
+                                         '--no-discordant'  : True,
+                                         '--no-mixed'       : True
+                                },
+                                SOAP: {
+                                        '-x' : options.max_insert_size,
+                                        '-m' : options.min_insert_size if options.min_insert_size > 0 else 100
+                                }}[options.aligner],
+                               # integrating 'rmappe' is different from others
+                                **aligner_options)
+
+        aligner_command = aligner_exec + aligner_options_string() + \
+                              { BOWTIE   : ' %(reference_genome)s  -f -1 %(input_file_1)s -2 %(input_file_2)s %(output_file)s',
+                                BOWTIE2  : ' -x %(reference_genome)s  -f -1 %(input_file_1)s -2 %(input_file_2)s -S %(output_file)s',
+                                SOAP     : ' -D %(reference_genome)s.fa.index -o %(output_file)s -a %(input_file_1)s -b %(input_file_2)s -2 %(output_file)s.unpaired' #,
+                              #  RMAP     : #  rmappe, also paste two inputs into one file.
+                             }[options.aligner]
+
+        logm('Aligner command: %s' % aligner_command)
+
+        bs_pair_end(options.infilename_1,
+                    options.infilename_2,
+                    asktag,
+                    options.adapter_file,
+                    options.cutnumber1,
+                    options.cutnumber2,
+                    options.no_split,
+                    str_no_mismatches,
+                    aligner_command,
+                    db_path,
+                    tmp_path,
+                    outfile,
+                    XS_pct,
+                    XS_count,
+                    options.Output_multiple_hit
+             )
+
+    outfile.close()
+